Plan for today


What you will learn

  • How to set up VS Code (and why?)
  • How to use basic Git-Github combo
  • How to use Quarto (in VS Code or RStudio)

What you will not learn

  • What is the absolute best setup
  • How to deal with the fact that co-authors use MS Word, Overleaf, etc.
  • What is the meaning of life

VS Code?



No, if

  • You only work in R

  • You do not want to pay entry costs

  • You get overwhelmed by the need for customization

Yes, if

  • You often have to jump between applications, e.g. RStudio or LaTeX editor

  • You find yourself using mouse too often

  • You often struggle to find the right command or option

VS Code!



  • One of the most used IDEs in the world (~14.24%) \(\Rightarrow\) Many extensions

  • Has extremely customizable interface

  • Has outstanding keyboard shortcuts customization

  • Works with anything (even has packages for Overleaf and Mathematica)

  • Has an (overwhelming) number of packages working with LLMs

Let’s go get it

  • Install VS Code at code.visualstudio.com/download

  • Install languageserver in R

  • Install the R extension for Visual Studio Code

    • Code completion (IntelliSense) works out of the box!
  • To enhance the experience of using R in VS Code, the following packages are recommended:

    • radian: A modern R console that corrects many limitations of the official R terminal and supports many features such as syntax highlighting and auto-completion

    • httpgd: An R package to provide a graphics device that asynchronously serves SVG graphics via HTTP and WebSockets. This package is required by the interactive plot viewer of the R extension for VS Code

What is Git?

Git + GitHub

  • Version Control: Provides a robust system that tracks changes and manages project history.

  • Branching and Merging: Supports branching and merging, enabling isolated development of features or fixes.

  • History and Reversion: Maintains a detailed history of changes, allowing easy reversion to previous states.

  • Offline Work: Allows for offline work with local repositories.

Dropbox/Overleaf/Google Docs

  • Real-time Collaboration: More suited for simpler, real-time collaboration.

  • Limited Branching: Does not inherently support branching and merging.

  • Basic Versioning: Focuses on file versioning without detailed change tracking.

  • Online Requirement: Requires internet access for syncing and collaboration.

Git?

No, if

  • Project is primarily individual and does not involve extensive collaboration.

  • Not comfortable with command-line tools or prefer simpler file management systems.

Yes, if

  • Multiple co-authors and need to track changes in documents AND data

  • Need to maintain a clear history of your project’s development and revisions.

  • You require a reliable backup system for your research files.

Different projects

No, if

%%{init: {
  'theme': 'base',
  'gitGraph': {'showCommitLabel': false, 'parallelCommits': true}
  } }%%
gitGraph
   commit id: "Initial commit" tag: "Initial"
   commit
   commit tag: "Pretty figures"
   commit
   commit tag: "Journal submission"

Yes, if

%%{init: {
  'theme': 'base',
  'gitGraph': {'showCommitLabel': false, 'parallelCommits': true}
  } }%%
gitGraph
   commit id: "Initial commit" tag: "Initial"
   commit
   branch Jimbo
   checkout Jimbo
   commit tag: "Nice figures"
   checkout main
   branch Gosha
   checkout Gosha
   commit
   checkout main
   merge Jimbo
   commit
   checkout Gosha
   merge main
   commit tag: "Code speedup"
   checkout Jimbo
   commit
   checkout main
   merge Gosha
   merge Jimbo
   commit tag: "Journal submission"

But how does Jimbo get access?

  • via a remote Hub, like GitHub:
  1. Create a GitHub repo (if does not exist already)
git init 

(under the hood)

  1. Create a local copy of the repo
git clone <repository-url> 
  1. Do some work

Git won’t help

  1. Stage and Commit your work
    • (optionally) selectively save files to commit to logically categorize work
git add <file-name> # or . to add everything
git commit -m "Your commit message"
  1. Push your work back
git push
  • We can interact with git directly via command line (terminal), or IDE like RStudio or VS Code

Git branching


Creating and Switching Branches

  • Create a new branch:

    git branch <branch-name>
  • Switch to a branch:

    git checkout <branch-name>
  • Create and switch to a new branch:

    git checkout -b <branch-name>

Merging Branches

  • Merge a branch into the current branch:

    git merge <branch-name>
  • Delete a branch after merging:

    git branch -d <branch-name>
  • Force delete a branch:

    git branch -D <branch-name>

One does not simply…

You Don’t Need to Remember All Git Commands

  • It’s impossible to remember every single Git command
  • Focus on mastering a few essential commands
  • Use git help or online resources for the rest
  • Embrace the power of AI and auto-complete from history

Let’s go get it



Quarto?

  • An open-source scientific and technical publishing system

  • Allows you to bring together everything:

    • LaTeX + Markdown + HTML for text editing
    • R/Python/Julia for statistics
    • Produce manuscripts, presentations, dashboards, websites…
    • Produce output in PDF, HTML or Word format

There is no reason not to switch beyond entry costs!

Quarto!

  1. It is fairly easy to start the switch

    • If you used R Markdown before, then it is backward compatible
    • If you used raw LaTeX the only new thing to learn how to switch is YAML preamble
  1. It is better than alternative in any respect

    • It is more versatile
    • Easier to read
    • Has Visual editor (for those who remember LyX)
    • Allow to do many things (papers, presentation, code, webpages)
    • Forces you to learn new useful things (e.g. YAML and HTML)

Papers


  • Write papers as normal

  • Use executable chunks with code ```

  • Use Markdown natively, e.g. 

    • * around word will make it italic and ** will make it bold
    • # for section, ## for subsection, etc.
    • []() for links and ![]() for images

Presentations



  • beamer for LaTeX slides

  • Powerpoint for when you have to collaborate via Office

  • Revealjs – essentially the replacement for xaringan, but with Pandoc-native syntax

Revealjs



  • revealjs is an open source HTML presentation framework

  • Enables anyone with a web browser to create fully-featured and beautiful presentations for free.

  • revealjs for Quarto is a framework for turning Pandoc-friendly markdown + code into beautiful slides

  • Shines when used for interactive slides, data results and math

Executable code

library(ggplot2)
ggplot(mtcars, aes(hp, mpg, color = am)) +
  geom_point() +
  geom_smooth(formula = y ~ x, method = "loess")

Pretty code

  • Over 20 syntax highlighting themes available
  • Default theme optimized for accessibility
# Define a server for the Shiny app
function(input, output) {
  
  # Fill in the spot we created for a plot
  output$phonePlot <- renderPlot({
    # Render a barplot
  })
}

Code animations

  • Over 20 syntax highlighting themes available
  • Default theme optimized for accessibility
# Define a server for the Shiny app
function(input, output) {
  
  # Fill in the spot we created for a plot
  output$phonePlot <- renderPlot({
    # Render a barplot
    barplot(WorldPhones[,input$region]*1000, 
            main=input$region,
            ylab="Number of Telephones",
            xlab="Year")
  })
}

LaTeX equations

MathJax rendering of equations to HTML

\begin{gather*}
a_1=b_1+c_1\\
a_2=b_2+c_2-d_2+e_2
\end{gather*}

\begin{align}
a_{11}& =b_{11}&
  a_{12}& =b_{12}\\
a_{21}& =b_{21}&
  a_{22}& =b_{22}+c_{22}
\end{align}
\[\begin{gather*} a_1=b_1+c_1\\ a_2=b_2+c_2-d_2+e_2 \end{gather*}\] \[\begin{align} a_{11}& =b_{11}& a_{12}& =b_{12}\\ a_{21}& =b_{21}& a_{22}& =b_{22}+c_{22} \end{align}\]

Markdown tables

| Default | Left | Right | Center |
|---------|:-----|------:|:------:|
| 12      | 12   |    12 |   12   |
| 123     | 123  |   123 |  123   |
| 1       | 1    |     1 |   1    |

: Demonstration of pipe table syntax
Demonstration of pipe table syntax
Default Left Right Center
12 12 12 12
123 123 123 123
1 1 1 1

Tabsets

mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4
Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4
Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1
Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1
Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2
Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1
Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4
Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2
Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2
Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4
Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4
Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3
Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3
Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3
Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4
Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4
Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4
Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1
Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2
AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2
Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4
Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2
Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1
Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2
Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2
Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4
Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6
Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8
Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2

Interactive slides

Include Jupyter widgets and htmlwidgets in your presentations

Let’s go get it



  • Additionally, you can download and install Quarto using:
Bash
brew install quarto
PowerShell
choco install quarto